[BioC] pdInfoBuilder -- MOUSEDIVm520650

[Benilton Carvalho]

Dear Robert,

the story is a bit more complicated than that. But to be objective,
here's the summary:

The information used by the crlmm package requires you to have a
training dataset (on the human case, we use HapMap). With this
reference set, we estimate a number of parameters that go into
annotation package.

Then, once the annotation package is created, you'll be able to run
crlmm on the dataset you refer to.

Because this is not a trivial task, I'm happy to discuss with you
(off-list) some further details.

b

On 27 May 2010 13:53, Ivanek, Robert <robert.ivanek at fmi.ch> wrote:
> Dear BioC list,
>
> I would like to create the annotation package for Affymetrix Mouse
> Diversity Array (MOUSEDIVm520650) and run CNV analysis on these arrays.
>
> However I am missing three files, which are required to successfully
> build the annotation package and run the analysis.
>
> splineParamFile
> crlmmInfoFile
> referenceDistFile
>
> Based on the description in pdInfoBuilder reference manual they are
> required to run the crlmm function (from the crlmm package).
> Usually the files are available at the svn repository (described in the
> pdInfoBuilder reference manual)
> https://hedgehog.fhcrc.org/bioc-data/trunk/annotation/parms_store
> I could not access this svn repository (readonly account + password does
> not work). Could somebody provide me these files?
>
> Best regards
>
> Robert
>
>
> --
> Robert Ivanek
> Postdoctoral Fellow Schuebeler Group
> Friedrich Miescher Institute
> Maulbeerstrasse 66
> 4058 Basel / Switzerland
> Office phone: +41 61 697 6100
>
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